Hi All,
I need to sort the bam file by read name before I can use bamToFastq for my
paired end sequences.
1. My bam files is coordinate sorted as shown here
> samtools view -H HBS0001.bam | grep SO
@HD VN:1.0 GO:none SO:coordinate
2. But after I executed the following command, no output file is founded
> samtools sort -n HBS0001.bam -o HBS0001.namSort.bam
3. my large log file contains the following non-readable characters
> head log.0.o183860
[bam_sort_core] merging from 104 files...
?BCsmV]??E>?mn~[XAEADD7!-3s??})???}??%? ۚ?Ƣ? k?E&
f????]?݄yg?]F?ԝ?B7eIH???~???????<g??yޙs?ȪnߩA???kڛG;rH??m??j?m?07??????S??cO??F;?=?O???(?J
?dF?H??-f.?;?+2?"!?&eMF?p?K?L????a?06#lAh/??o?
?
?g???TÙ?E???H??M?,!??????
:-??9????;?r&?/,?הg)c?Bi???C?B/P??y???I鵒?X??
kն?)?]J?
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u\?|?χ???X?Gh<?<?noCWeiߺѬ?XHG???j?<?D|?h?s???6??
è?^J,T ?ձ?
?\??I??YQ)6??tXY(??Z?j??jD??{r???r??6??????m\M??y???E՜^|?O?koX?Y?Z??222>>?krvJ
?Mk??!G:ݑ??N???7???8??4Z???T
?7??4<\?jf?@??????]Y?}{e)?6s??d!l???@?YY?<PYV}?}I?,\???[??`x????pl????R?~v??$LO??J????,?/S????Rr[?Ƶ7Ӆ
?!?X?}??%?o??????/+
ug?m?5p?L_??????ڷ9??û?l6????ZMX???20???p?X?&?7??d??7݆??
8}??6?x?V"?\??d+??;?j??L???"7? ????o???}
L???
Thank you very much for your help!
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